The Tigers levelled twice as Jon Parkin and Stuart Elliott cancelled out strikes by Matt Harrold and Freddy Eastwood.
And despite having skipper Ian Ashbee sent off for a late tackle, Craig Fagan's goal ensured it was a Halloween of no treats for the Shrimpers.
Clear-cut chances were at a premium early on as Southend's Eastwood blazed wide before Parkin and Dean Marney's efforts from distance failed to trouble Blues goalkeeper Darryl Flahavan.
The Tigers looked to have made the breakthrough on 15 minutes but Michael Turner flashed his header just wide of the far post from Marney's corner from the left.
The match was punctuated by frequent free-kicks and Gower's one from the right was missed by City keeper Boaz Myhill, but Efe Sodje's free header went over the crossbar.
Parkin's hooked shot then went narrowly wide before Southend opened the scoring on 28 minutes.
Eastwood's cross-field ball picked out Gower on the left, who beat Sam Ricketts to deliver the ball into Harrold's path. He tapped home from six yards for his second goal of the season.
The lead lasted just seven minutes before Ashbee made the most of a poor Lewis Hunt clearance to lay the ball off to Parkin who fired into the bottom right-hand corner for his sixth goal of the season.
Southend got the perfect start to the second half thanks to a bit of Eastwood magic.
The forward has attracted interest from a host of clubs and showed why when he picked up Sodje's pass, turned the Tigers' defence and slotted home from 16 yards for his ninth of the season on 51 minutes.
Again the lead proved short-lived for the hosts as Hull were on terms five minutes later.
Adam Barrett conceded a free-kick 25 yards out and Elliott's dead ball kick took a deflection off the Southend wall and left Flahavan with no chance.
Having twice come back, the Tigers suffered a further setback on 57 minutes when skipper Ashbee was given a straight red card for a late challenge on Harrold.
But going to ten men did not trouble Phil Parkinson's troops as they took the lead for the first time on 65 minutes.
Craig Fagan burst through the midfield, exchanged passes with Sam Ricketts on the right wing and then slammed the ball past Flahavan from ten yards.
Gower fired inches over the crossbar before Steve Tilson threw on Luke Guttridge and Gary Hooper in place of the ineffective Peter Clarke and Simon Francis.
Eastwood's rising shot was then superbly saved by a diving Myhill before Guttridge fizzed a free-kick inches wide of the left.
Eastwood then thumped another free-kick just wide, but Hull resisted a late barrage from the Blues to secure their first win in six games.